Thermo Scientific™ Orbitrap Exploris™ 240 mass spectrometer - Faster time to results–intelligent data acquisition and processing with applications software

Significance of the topic

The emergence of high-resolution, accurate-mass multiplexed proteomics addresses critical needs in pharmaceutical development, biomarker discovery, and systems biology. Combining isobaric tagging with advanced mass analyzers enables researchers to profile dynamic proteome changes across numerous samples in a single experiment, reducing instrument time and increasing data consistency.

Objectives and study overview

This study evaluates the performance of the Thermo Scientific Orbitrap Exploris 240 mass spectrometer in conjunction with TMTpro 16plex isobaric tags. Key goals include demonstrating rapid data acquisition, high quantitative precision, and streamlined workflows from sample preparation to final data analysis, benchmarked against conventional proteomics solutions.

Used instrumentation

• Orbitrap Exploris 240 mass spectrometer
• FAIMS Pro interface (compensation voltages –60V/–80V)
• EASY-nLC 1200 chromatography system
• EASY-Spray source and NanoSpray Flex ion source
• Sonation column oven at 40 °C with a 25 cm IonOpticks Aurora column

Main results and discussion

Quantitative analysis of starved HeLa cells under four treatment conditions and a pooled reference channel achieved approximately 4 000 proteins quantified across 16 samples in a single 120 min LC-MS run without missing values. Optimized method templates and Proteome Discoverer processing (1 % PSM FDR, 10 ppm precursor tolerance) yielded high-confidence reporter ion intensities. Principal component analysis resolved distinct treatment clusters, and hierarchical clustering confirmed reproducible separation of knockout protein profiles. The integration of FAIMS Pro enhanced selectivity and signal‐to‐noise ratios.

Benefits and practical applications of the method

• High multiplex capacity: simultaneous quantification of up to 16 samples accelerates comparative proteomics studies.
• Improved throughput: streamlined instrument setup and ready‐to‐run templates reduce hands-on time.
• Robust quantitation: Orbitrap resolving power enables baseline separation of TMTpro reporter isotopologues at low m/z.
• End-to-end workflow: from sample multiplexing to automated data analysis supporting reproducible biomarker and drug target discovery.

Future trends and potential applications

Advancements may include expanded multiplexing beyond 16 channels, integration with automated sample preparation systems, and coupling with artificial intelligence–driven data analysis pipelines. Clinical proteomics and large-scale population studies will particularly benefit from increased throughput and standardized workflows.

Conclusion

The Thermo Scientific Orbitrap Exploris 240 MS combined with TMTpro 16plex reagents delivers a best-in-class solution for high-throughput proteome quantitation. Its intelligent acquisition strategies, high resolving power, and application-specific software enable rapid, accurate, and reproducible multiplexed analyses suitable for diverse research and quality control environments.

References

• Thermo Fisher Scientific. Proof of performance note XX-65862: Technical innovations in Orbitrap Exploris 240.
• Thermo Fisher Scientific. Proof of performance note XX-65879: Method templates for TMTpro 16plex workflows.